Headwords and suffixes in biomedical names

Manabu Torii, Hongfang Liu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

Natural Language Processing (NLP) techniques have been used for the task of extracting and mining knowledge from biomedical literature, One of the critical steps of such a task is biomedical named entity tagging (BNER) which usually contains two steps: the first step is the identification of biomedical names in text and the second is the assignment of semantic classes predefined to names identified by the first step. Headwords and suffixes have been used frequently by BNER systems as features for the assignment of semantic classes to names in text. However, there are few studies to evaluate the performance of headwords and suffixes in predicting semantic classes of biomedical terms utilizing knowledge sources in an unsupervised way. We conducted a study to evaluate the performance of headwords and suffixes using names in the Unified Medical Language System (UMLS) where the semantic classes associated with these names were obtained by modifying an existing UMLS semantic group system and incorporating the GENIA ontology. We define headwords and suffixes that are significantly associated with a specific semantic class as semantic suffixes. The performance of semantic assignment using semantic suffixes achieved an F-measure of 86.4% with a precision of 91.6% and a recall of 81.7%. When applying these semantic suffixes obtained using the UMLS to names extracted from the GENIA corpus, the system achieved an F-measure of 73.4% with a precision of 84.2% and a recall of 65.1% where these performance measures could be improved dramatically when limited to names associated with classes that have the corresponding GENIA types.

Original languageEnglish (US)
Title of host publicationKnowledge Discovery in Life Science Literature - PAKDD 2006 International Workshop, KDLL 2006, Proceedings
Pages29-41
Number of pages13
DOIs
StatePublished - Jul 10 2006
EventPAKDD 2006 International Workshop on Knowledge Discovery in Life Science Literature, KDLL 2006 - Singapore, Singapore
Duration: Apr 9 2006Apr 9 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3886 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

OtherPAKDD 2006 International Workshop on Knowledge Discovery in Life Science Literature, KDLL 2006
CountrySingapore
CitySingapore
Period4/9/064/9/06

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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    Torii, M., & Liu, H. (2006). Headwords and suffixes in biomedical names. In Knowledge Discovery in Life Science Literature - PAKDD 2006 International Workshop, KDLL 2006, Proceedings (pp. 29-41). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3886 LNBI). https://doi.org/10.1007/11683568_3